Fluorometric Quantification of Specific Chemical Species in Single Cells

1981 ◽  
pp. 251-293 ◽  
Author(s):  
Frank A. Dolbeare
Author(s):  
Prinessa Chellan ◽  
Peter J Sadler

Which elements are essential for human life? Here we make an element-by-element journey through the periodic table and attempt to assess whether elements are essential or not, and if they are, whether there is a relevant code for them in the human genome. There are many difficulties such as the human biochemistry of several so-called essential elements is not well understood, and it is not clear how we should classify elements that are involved in the destruction of invading microorganisms, or elements which are essential for microorganisms with which we live in symbiosis. In general, genes do not code for the elements themselves, but for specific chemical species, i.e. for the element, its oxidation state, type and number of coordinated ligands, and the coordination geometry. Today, the biological periodic table is in a position somewhat similar to Mendeleev's chemical periodic table of 1869: there are gaps and we need to do more research to fill them. The periodic table also offers potential for novel therapeutic and diagnostic agents, based on not only essential elements, but also non-essential elements, and on radionuclides. Although the potential for inorganic chemistry in medicine was realized more than 2000 years ago, this area of research is still in its infancy. Future advances in the design of inorganic drugs require more knowledge of their mechanism of action, including target sites and metabolism. Temporal speciation of elements in their biological environments at the atomic level is a major challenge, for which new methods are urgently needed.


Author(s):  
Tadashi Tokuhiro ◽  
Josh W. Carey ◽  
Massimo Bertino ◽  
Akira Tokuhiro

Within the management of radioactive waste, we sought to consider a new approach radioactive hazardous waste processing in aqueous or similar (low-level waste; LLW) forms LLW and in fact, ‘contaminants of concern’ is often stored as diluted aqueous solutions of radioactive (or non) elements and contained in storage containers. One of the general problems associated with mixed liquid waste is the lack of an efficient, effective, and inexpensive means of processing (separating) its constituents. Two of the objectives in processing solid, radioactive laden liquid LLW are as follows: 1) to separate/extract the radioisotopes from the rest of the mixed constituents, and 2) to produce stable solidified forms encapsulating radioactive elements. Recent R&D in the physical chemistry of gel materials, have identified promising approach to simultaneously achieve the above objectives. That is, by utilizing and manipulating the physicochemical properties of various silica- and polymer-based gels at the nanoscale, we have demonstrated a process by which to specific chemical species are encapsulated.


Author(s):  
Fabian N. Murrieta-Rico ◽  
Vitalii Petranovskii ◽  
Rosario I. Yocupicio-Gaxiola ◽  
Vera Tyrsa

The detection of chemical species is a common and required task in several areas of technology. Currently, measurements in dedicated labs are the predominant tools for detection and characterization of chemicals and materials. Although these techniques are available in specialized equipment, their use is often bounded by cost of application or the operator's expertise. Also, in many applications rather than an analysis of all the detectable chemical species, it is only of interest to determine the presence of a particular chemical compound, and if it is present, to quantify its concentration. For these reasons, alternative methods for detecting specific chemical species are required. One case of such methods are the optical chemical sensors, particularly the ones based on the materials known as zeolites. In a broad sense, these sensors are constituted by an optical detector that is modified with zeolites. This combination allows the detection of specific chemical compounds if the zeolitic materials is properly modified to have an optical response for the analyte.


1999 ◽  
Vol 202 (4) ◽  
pp. 333-341 ◽  
Author(s):  
L.L. Moroz ◽  
R. Gillette ◽  
J.V. Sweedler

Understanding the role of the gaseous messenger nitric oxide (NO) in the nervous system is complicated by the heterogeneity of its nerve cells; analyses carried out at the single cell level are therefore important, if not critical. Some invertebrate preparations, most especially those from the gastropod molluscs, provide large, hardy and identified neurons that are useful both for the development of analytical methodologies and for cellular analyses of NO metabolism and its actions. Recent modifications of capillary electrophoresis (CE) allow the use of a small fraction of an individual neuron to perform direct, quantitative and simultaneous assays of the major metabolites of the NO-citrulline cycle and associated biochemical pathways. These chemical species include the products of NO oxidation (NO2-/NO3-), l-arginine, l-citrulline, l-ornithine, l-argininosuccinate, as well as selected NO synthase inhibitors and cofactors such as NADPH, biopterin, FMN and FAD. Diverse cotransmitters can also be identified in the same nitrergic neuron. The sensitivity of CE methods is in the femtomole to attomole range, depending on the species analysed and on the specific detector used. CE analysis can be combined with prior in vivo electrophysiological and pharmacological manipulations and measurements to yield multiple physiological and biochemical values from single cells. The methodologies and instrumentation developed and tested using the convenient molluscan cell model can be adapted to the smaller and more delicate neurons of other invertebrates and chordates.


Author(s):  
Rafael E. Villegas-Villegas ◽  
Alejandra Baldi-Sevilla ◽  
José Pablo Aguiar-Moya ◽  
Luis Loria-Salazar

The chemical changes that occur to asphalt with oxidation include an increase in oxygen content, as well as the unsaturation of the molecules. This change raises the polarity and stiffness of the material. As a consequence, the elastic response increases, altering its rheology. These transformations are essential to determine pavement performance during its service life. However, the characterization of these chemical and rheological processes cannot be completed because of the inefficiency of current procedures that simulate asphalt oxidation. For this reason, the objective of this study is to characterize asphalt oxidation fundamentally and to relate the observed changes in the materials’ mechanical response. To achieve this goal, a representative group of asphalt samples has been exposed to environmental oxidation, and alternatively to thermal and ultraviolet aging in the laboratory. The samples were characterized chemically and rheologically before the start of the experiment. It was possible to find a correlation between the content of specific chemical species in the material and their mechanical behavior at low and intermediate temperatures. In addition, the present study helps to understand the oxidation phenomena, and helps verify the ineffectiveness of traditional aging techniques, so that they can be modified to simulate the environmental process better.


Materials ◽  
2018 ◽  
Vol 11 (8) ◽  
pp. 1389 ◽  
Author(s):  
Luyao Huang ◽  
Ziyu Li ◽  
Yuntian Lou ◽  
Fahe Cao ◽  
Dawei Zhang ◽  
...  

Scanning electrochemical microscopy (SECM) is a chemical microscopy technique with high spatial resolution for imaging sample topography and mapping specific chemical species in liquid environments. With the development of smaller, more sensitive ultramicroelectrodes (UMEs) and more precise computer-controlled measurements, SECM has been widely used to study biological systems over the past three decades. Recent methodological breakthroughs have popularized SECM as a tool for investigating molecular-level chemical reactions. The most common applications include monitoring and analyzing the biological processes associated with enzymatic activity and DNA, and the physiological activity of living cells and other microorganisms. The present article first introduces the basic principles of SECM, followed by an updated review of the applications of SECM in biological studies on enzymes, DNA, proteins, and living cells. Particularly, the potential of SECM for investigating bacterial and biofilm activities is discussed.


2007 ◽  
Vol 7 (6) ◽  
pp. 17069-17097
Author(s):  
P. Jöckel ◽  
A. Kerkweg ◽  
J. Buchholz ◽  
H. Tost ◽  
R. Sander ◽  
...  

Abstract. The implementation of processes related to chemistry into Earth System Models and their coupling within such systems requires the consistent description of the chemical species involved. We provide a tool (written in Fortran95) to structure and manage information about constituents, herein after referred to as tracers, namely the Modular Earth Submodel System (MESSy) generic (i.e., infrastructure) submodel TRACER. With TRACER it is possible to define a multitude of tracer sets, depending on the spatio-temporal representation (i.e., the grid structure) of the model. The required information about a specific chemical species is split into the static meta-information about the characteristics of the species, and its (generally in time and space variable) abundance in the corresponding representation. TRACER moreover includes two submodels. One is TRACER_FAMILY, an implementation of the tracer family concept. It distinguishes between two types: type-1 families are usually applied to handle strongly related tracers (e.g., fast equilibrating species) for a specific process (e.g., advection). In contrast to this, type-2 families are applied for tagging techniques, in which specific species are artificially decomposed and associated with additional information, in order to conserve the linear relationship between the family and its members. The second submodel is TRACER_PDEF, which corrects and budgets numerical negative overshoots that arise in many process implementations due to the numerical limitations (limited precision, rounding errors). The submodel therefore guarantees the positive definiteness of the tracers and stabilises the integration scheme. As a by-product, it further provides a global tracer mass diagnostic. Last but not least, we present the submodel PTRAC for the definition of prognostic tracers via a Fortran95 namelist. TRACER with its submodels and PTRAC can readily be applied to a variety of models without further requirements. The code and a documentation is included in the electronic supplement.


mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Christopher R. Anderton ◽  
Jennifer M. Mobberley ◽  
Jessica K. Cole ◽  
Jamie R. Nunez ◽  
Robert Starke ◽  
...  

ABSTRACT Increasing anthropogenic inputs of fixed nitrogen are leading to greater eutrophication of aquatic environments, but it is unclear how this impacts the flux and fate of carbon in lacustrine and riverine systems. Here, we present evidence that the form of nitrogen governs the partitioning of carbon among members in a genome-sequenced, model phototrophic biofilm of 20 members. Consumption of NO3− as the sole nitrogen source unexpectedly resulted in more rapid transfer of carbon to heterotrophs than when NH4+ was also provided, suggesting alterations in the form of carbon exchanged. The form of nitrogen dramatically impacted net community nitrogen, but not carbon, uptake rates. Furthermore, this alteration in nitrogen form caused very large but focused alterations to community structure, strongly impacting the abundance of only two species within the biofilm and modestly impacting a third member species. Our data suggest that nitrogen metabolism may coordinate coupled carbon-nitrogen biogeochemical cycling in benthic biofilms and, potentially, in phototroph-heterotroph consortia more broadly. It further indicates that the form of nitrogen inputs may significantly impact the contribution of these communities to carbon partitioning across the terrestrial-aquatic interface. IMPORTANCE Anthropogenic inputs of nitrogen into aquatic ecosystems, and especially those of agricultural origin, involve a mix of chemical species. Although it is well-known in general that nitrogen eutrophication markedly influences the metabolism of aquatic phototrophic communities, relatively little is known regarding whether the specific chemical form of nitrogen inputs matter. Our data suggest that the nitrogen form alters the rate of nitrogen uptake significantly, whereas corresponding alterations in carbon uptake were minor. However, differences imposed by uptake of divergent nitrogen forms may result in alterations among phototroph-heterotroph interactions that rewire community metabolism. Furthermore, our data hint that availability of other nutrients (i.e., iron) might mediate the linkage between carbon and nitrogen cycling in these communities. Taken together, our data suggest that different nitrogen forms should be examined for divergent impacts on phototrophic communities in fluvial systems and that these anthropogenic nitrogen inputs may significantly differ in their ultimate biogeochemical impacts.


2008 ◽  
Vol 8 (6) ◽  
pp. 1677-1687 ◽  
Author(s):  
P. Jöckel ◽  
A. Kerkweg ◽  
J. Buchholz-Dietsch ◽  
H. Tost ◽  
R. Sander ◽  
...  

Abstract. The implementation of processes related to chemistry into Earth System Models and their coupling within such systems requires the consistent description of the chemical species involved. We provide a tool (written in Fortran95) to structure and manage information about constituents, hereinafter referred to as tracers, namely the Modular Earth Submodel System (MESSy) generic (i.e., infrastructure) submodel TRACER. With TRACER it is possible to define a multitude of tracer sets, depending on the spatio-temporal representation (i.e., the grid structure) of the model. The required information about a specific chemical species is split into the static meta-information about the characteristics of the species, and its (generally in time and space variable) abundance in the corresponding representation. TRACER moreover includes two submodels. One is TRACER_FAMILY, an implementation of the tracer family concept. It distinguishes between two types: type-1 families are usually applied to handle strongly related tracers (e.g., fast equilibrating species) for a specific process (e.g., advection). In contrast to this, type-2 families are applied for tagging techniques. Tagging means the artificial decomposition of one or more species into parts, which are additionally labelled (e.g., by the region of their primary emission) and then processed as the species itself. The type-2 family concept is designed to conserve the linear relationship between the family and its members. The second submodel is TRACER_PDEF, which corrects and budgets numerical negative overshoots that arise in many process implementations due to the numerical limitations (e.g., rounding errors). The submodel therefore guarantees the positive definiteness of the tracers and stabilises the integration scheme. As a by-product, it further provides a global tracer mass diagnostic. Last but not least, we present the submodel PTRAC, which allows the definition of tracers via a Fortran95 namelist, as a complement to the standard tracer definition by application of the TRACER interface routines in the code. TRACER with its submodels and PTRAC can readily be applied to a variety of models without further requirements. The code and a documentation are included in the electronic supplement.


2021 ◽  
Vol 13 (8) ◽  
pp. 1437-1444
Author(s):  
Jeonghun Kim ◽  
So Yeon Ahn ◽  
Soong Ho Um

Numerous heat-dependent chemical reactions are involved in organismal life, and temperature is an important factor that determines whether such reactions progress. To date, ultrasound and thermotherapy techniques have been established in high-end medical treatments and are proposed to monitor temperature changes on a nanoscale of localized areas such as single cells and to induce material synthesis due to local energy conversion. In this study, a nanoprobe that can measure the local temperature on the nanoscale is designed and developed using gold nanoparticles and thermo-sensitive fluorescent materials. To support this concept, a polymer capable of controlling the physical properties of gold nanorods (AuNRs) is manufactured using light-heat conversion synthesis.


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